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Table 1 Significantly mutated genes identified by DOTS-Finder in four cancer types

From: DOTS-Finder: a comprehensive tool for assessing driver genes in cancer genomes

Acute myeloid leukemia (S = 196, MNSp = 11) Thyroid carcinoma (S = 326, MNSp = 19) Breast cancer (S = 1046, MNSp = 36) Bladder carcinoma (S = 145, MNSp = 177)
Gene name NS frequency q-value Gene name NS frequency q-value Gene name NS frequency q-value Gene name NS frequency q-value
TSGs            
CEBPA 0.066 0 TG 0.049 8.0E-10 CBFB 0.021 0 ARID1A 0.241 0
NPM1 0.276 0 EMG1 0.018 5.3E-08 CDH1 0.062 0 CDKN1A 0.145 0
RUNX1 0.092 0 RPTN 0.025 9.1E-06 GATA3 0.095 0 KDM6A 0.214 0
TET2 0.087 0 PPM1D 0.015 0.0054 MAP2K4 0.039 0 TP53 0.262 0
TP53 0.077 0 TMCO2 0.009 0.0056 MAP3K1 0.070 0 ELF3 0.076 1.2E-10
WT1 0.061 0 IL32 0.009 0.0152 PTEN 0.040 0 MLL2 0.262 1.2E-10
RAD21 0.026 3.3E-06 DNMT3A 0.015 0.2896 TP53 0.338 0 EP300 0.152 3.0E-09
PHF6 0.031 3.4E-06   TBX3 0.022 1.1E-12 RB1 0.110 2.3E-08
STAG2 0.031 1.4E-05     MLL3 0.065 5.9E-12 SPTAN1 0.097 3.0E-06
EZH2 0.015 0.0007     AOAH 0.019 3.9E-10 MLL3 0.200 6.1E-06
ASXL1 0.026 0.0014     CTCF 0.021 7.9E-10 CREBBP 0.131 1.2E-05
HNRNPK 0.010 0.0083     RUNX1 0.024 3.2E-06 STAG2 0.090 7.6E-05
CALR 0.010 0.0142     NCOR1 0.038 3.9E-06 FOXQ1 0.048 0.0060
CBFB 0.010 0.0572     RB1 0.021 6.1E-06 TXNIP 0.055 0.0079
CBX7 0.005 0.0948     NCOR2 0.032 0.0003 FAT1 0.110 0.0370
BCOR 0.010 0.1971     STXBP2 0.010 0.0004 FBXW7 0.069 0.0428
     AQP7 0.008 0.0017 GCC2 0.069 0.0800
       ZFP36L1 0.012 0.0046 ZNF513 0.055 0.0911
       RBMX 0.012 0.0056 KLF5 0.062 0.1184
       GPS2 0.007 0.0095 GPS2 0.028 0.2599
       CASP8 0.015 0.0104 NHLRC1 0.021 0.2635
       CDKN1B 0.008 0.0125  
       UBC 0.008 0.0155    
       MED23 0.013 0.0224    
       MYB 0.012 0.0407    
       CCDC144NL 0.008 0.1268    
       GNRH2 0.003 0.2062    
       HNF1A 0.009 0.7280    
OGs            
CEBPA 0.066 0 BRAF 0.561 0 AKT1 0.022 0 TP53 0.262 0
DNMT3A 0.260 0 HRAS 0.037 0 PIK3CA 0.285 0 NFE2L2 0.076 6.1E-06
FLT3 0.270 0 NRAS 0.080 0 TP53 0.338 0 ERBB3 0.117 1.1E-05
IDH1 0.097 0 TG 0.049 3.5E-08 TBX3 0.022 9.0E-10 RARG 0.069 1.5E-05
IDH2 0.102 0 DNASE2 0.009 0.0694 SF3B1 0.017 3.4E-08 IRS4 0.014 0.6550
NRAS 0.077 0 PRDM9 0.018 0.0816 FOXA1 0.017 7.7E-05 ELP5 0.014 0.6550
TP53 0.077 0 DICER1 0.009 0.1070 HIST1H3B 0.008 0.0001 RPS6 0.021 0.6550
U2AF1 0.041 0 ZNF845 0.018 0.1070 MEF2A 0.014 0.0002    
    PRG4 0.012 0.1085 PIK3R1 0.025 0.0008    
    PTTG1IP 0.012 0.1085 ATN1 0.017 0.0425    
       AKD1 0.018 0.0431    
  1. MNSp, median number of non-silent mutations per patient; NS freq, non-synonymous mutation frequency among samples; S, number of samples. Genes in bold are the closest to significance in the ranking.